pip3 install pandas failing in gitlab-ci.yaml
It is failing as shown below, pasting logs. I am getting this error once I run my yaml file, for rest of the pip install it is working fine. It is failing only for Pandas.
I have left it like this for hours, with no progress, what is wrong?
Without success, I have tried:
Pip Install hangs
https://bbs.archlinux.org/viewtopic.php?id=174186
$ pip3 install pymysql
Collecting pymysql
Downloading PyMySQL-1.0.2-py3-none-any.whl (43 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.8/43.8 KB 7.5 MB/s eta 0:00:00
Installing collected packages: pymysql
Successfully installed pymysql-1.0.2
$ pip uninstall numpy
WARNING: Skipping numpy as it is not installed.
$ pip3 install pandas
Collecting pandas
Downloading pandas-1.4.1.tar.gz (4.9 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.9/4.9 MB 52.8 MB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'error'
error: subprocess-exited-with-error
× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> [308 lines of output]
Collecting setuptools>=51.0.0
Using cached setuptools-60.9.3-py3-none-any.whl (1.1 MB)
Collecting wheel
Using cached wheel-0.37.1-py2.py3-none-any.whl (35 kB)
Collecting Cython<3,>=0.29.24
Using cached Cython-0.29.28-cp39-cp39-musllinux_1_1_x86_64.whl (2.1 MB)
Collecting oldest-supported-numpy>=0.10
Downloading oldest_supported_numpy-2022.1.30-py3-none-any.whl (3.9 kB)
Collecting numpy==1.19.3
Downloading numpy-1.19.3.zip (7.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.3/7.3 MB 73.0 MB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'error'
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [276 lines of output]
Running from numpy source directory.
setup.py:480: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
run_build = parse_setuppy_commands()
Processing numpy/random/_bounded_integers.pxd.in
Processing numpy/random/_mt19937.pyx
Processing numpy/random/_generator.pyx
Processing numpy/random/_philox.pyx
Processing numpy/random/_bounded_integers.pyx.in
blas_opt_info:
blas_mkl_info:
customize UnixCCompiler
libraries mkl_rt not found in ['/builds/gp-cpg-iot/datawarehouse/data-pipelines/kolo-device-dimension-qr-update/venv/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
blis_info:
libraries blis not found in ['/builds/gp-cpg-iot/datawarehouse/data-pipelines/kolo-device-dimension-qr-update/venv/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
openblas_info:
libraries openblas not found in ['/builds/gp-cpg-iot/datawarehouse/data-pipelines/kolo-device-dimension-qr-update/venv/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
atlas_3_10_blas_threads_info:
Setting PTATLAS=ATLAS
libraries tatlas not found in ['/builds/gp-cpg-iot/datawarehouse/data-pipelines/kolo-device-dimension-qr-update/venv/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
atlas_3_10_blas_info:
libraries satlas not found in ['/builds/gp-cpg-iot/datawarehouse/data-pipelines/kolo-device-dimension-qr-update/venv/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in ['/builds/gp-cpg-iot/datawarehouse/data-pipelines/kolo-device-dimension-qr-update/venv/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
flame_info:
libraries flame not found in ['/builds/gp-cpg-iot/datawarehouse/data-pipelines/kolo-device-dimension-qr-update/venv/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
libraries lapack_atlas not found in /builds/gp-cpg-iot/datawarehouse/data-pipelines/kolo-device-dimension-qr-update/venv/lib
libraries tatlas,tatlas not found in /builds/gp-cpg-iot/datawarehouse/data-pipelines/kolo-device-dimension-qr-update/venv/lib
libraries lapack_atlas not found in /usr/local/lib
libraries tatlas,tatlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries tatlas,tatlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib/
libraries tatlas,tatlas not found in /usr/lib/
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLE
atlas_3_10_info:
libraries lapack_atlas not found in /builds/gp-cpg-iot/datawarehouse/data-pipelines/kolo-device-dimension-qr-update/venv/lib
libraries satlas,satlas not found in /builds/gp-cpg-iot/datawarehouse/data-pipelines/kolo-device-dimension-qr-update/venv/lib
libraries lapack_atlas not found in /usr/local/lib
libraries satlas,satlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries satlas,satlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib/
libraries satlas,satlas not found in /usr/lib/
<class 'numpy.distutils.system_info.atlas_3_10_info'>
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
libraries lapack_atlas not found in /builds/gp-cpg-iot/datawarehouse/data-pipelines/kolo-device-dimension-qr-update/venv/lib
libraries ptf77blas,ptcblas,atlas not found in /builds/gp-cpg-iot/datawarehouse/data-pipelines/kolo-device-dimension-qr-update/venv/lib
libraries lapack_atlas not found in /usr/local/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib/
libraries ptf77blas,ptcblas,atlas not found in /usr/lib/
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE
atlas_info:
libraries lapack_atlas not found in /builds/gp-cpg-iot/datawarehouse/data-pipelines/kolo-device-dimension-qr-update/venv/lib
libraries f77blas,cblas,atlas not found in /builds/gp-cpg-iot/datawarehouse/data-pipelines/kolo-device-dimension-qr-update/venv/lib
libraries lapack_atlas not found in /usr/local/lib
libraries f77blas,cblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries f77blas,cblas,atlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib/
libraries f77blas,cblas,atlas not found in /usr/lib/
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE
lapack_info:
libraries lapack not found in ['/builds/gp-cpg-iot/datawarehouse/data-pipelines/kolo-device-dimension-qr-update/venv/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
/tmp/pip-install-vaexwiws/numpy_677c648f418b4b9ba0617c24747fe32e/numpy/distutils/system_info.py:1748: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
return getattr(self, '_calc_info_{}'.format(name))()
lapack_src_info:
NOT AVAILABLE
/tmp/pip-install-vaexwiws/numpy_677c648f418b4b9ba0617c24747fe32e/numpy/distutils/system_info.py:1748: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
return getattr(self, '_calc_info_{}'.format(name))()
NOT AVAILABLE
numpy_linalg_lapack_lite:
FOUND:
language = c
define_macros = [('HAVE_BLAS_ILP64', None), ('BLAS_SYMBOL_SUFFIX', '64_')]
/tmp/pip-build-env-mvp8ezwv/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py:275: UserWarning: Unknown distribution option: 'define_macros'
warnings.warn(msg)
running dist_info
running build_src
build_src
building py_modules sources
creating build
creating build/src.linux-x86_64-3.9
creating build/src.linux-x86_64-3.9/numpy
creating build/src.linux-x86_64-3.9/numpy/distutils
building library "npymath" sources
Could not locate executable gfortran
Could not locate executable f95
Could not locate executable ifort
Could not locate executable ifc
Could not locate executable lf95
Could not locate executable pgfortran
Could not locate executable nvfortran
Could not locate executable f90
Could not locate executable f77
Could not locate executable fort
Could not locate executable efort
Could not locate executable efc
Could not locate executable g77
Could not locate executable g95
Could not locate executable pathf95
Could not locate executable nagfor
don't know how to compile Fortran code on platform 'posix'
creating build/src.linux-x86_64-3.9/numpy/core
creating build/src.linux-x86_64-3.9/numpy/core/src
creating build/src.linux-x86_64-3.9/numpy/core/src/npymath
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npymath/npy_math_internal.h
adding 'build/src.linux-x86_64-3.9/numpy/core/src/npymath' to include_dirs.
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npymath/ieee754.c
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npymath/npy_math_complex.c
None - nothing done with h_files = ['build/src.linux-x86_64-3.9/numpy/core/src/npymath/npy_math_internal.h']
building library "npysort" sources
creating build/src.linux-x86_64-3.9/numpy/core/src/common
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/common/npy_sort.h
adding 'build/src.linux-x86_64-3.9/numpy/core/src/common' to include_dirs.
creating build/src.linux-x86_64-3.9/numpy/core/src/npysort
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npysort/quicksort.c
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npysort/mergesort.c
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npysort/timsort.c
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npysort/heapsort.c
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npysort/radixsort.c
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/common/npy_partition.h
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npysort/selection.c
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/common/npy_binsearch.h
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npysort/binsearch.c
None - nothing done with h_files = ['build/src.linux-x86_64-3.9/numpy/core/src/common/npy_sort.h', 'build/src.linux-x86_64-3.9/numpy/core/src/common/npy_partition.h', 'build/src.linux-x86_64-3.9/numpy/core/src/common/npy_binsearch.h']
building library "npyrandom" sources
building extension "numpy.core._multiarray_tests" sources
creating build/src.linux-x86_64-3.9/numpy/core/src/multiarray
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/multiarray/_multiarray_tests.c
building extension "numpy.core._multiarray_umath" sources
Traceback (most recent call last):
File "/tmp/tmp1gke7ac6_in_process.py", line 363, in <module>
main()
File "/tmp/tmp1gke7ac6_in_process.py", line 345, in main
raise SystemError(
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
Cleaning up file based variables
00:00
ERROR: Job failed: command terminated with exit code 1```
